In general, yes, you can use it for multilevel project. The simpliest way to do it: make one big compressed package with all your files and load it content in your main function, or even better, use 'autoload' feature of CR Pack (refer to the CR Pack Demo#9). Keep in mind, while using CR Pack that 3dgs engine searches for 'hardcoded' resources (like bmap=<...>) before any plugin loaded. To trick the engine and compress most files you must avoid such declarations and create needed resources at runtime (like bmap_create(...)).
But I cannot understand your project structure. What do you mean :"say i have all exe's for every level i created for my game"? You need one 'level' with 'main' script assigned (usually this is the dummy level or menu level), when you publish it you will get your project's exe. Other levels should be compiled (builded) only. I must to make another demo for multilevel project, I think...
By the way, you can provide me with download link to your project (mail me that link) and I can try to help you. I agree that I will not use any part of your project or artwork in my future work.